I played with this a bit more and it looks like using <KeyDown LAlt> all of my alt actions and then <KeyUp LAlt> works, but only if it's the only command being executed by that hotkey. I tested this out and the following code works fine

<hotkey F6>
<sendpc ip removed for post>
<sendwin EQ2>
<KeyDown LAlt>
<wait 100>
<Text 8>
<wait 1000>
<Text 9>
<wait 100>
<KeyUp LAlt>

But this code does not (I added in <Text 1> which just puts me into autoattack mode. I tried other actions and they had the same result)

<hotkey F6>
<sendpc ip removed for post>
<sendwin EQ2>
<Text 1>
<wait 100>
<KeyDown LAlt>
<wait 100>
<Text 8>
<wait 1000>
<Text 9>
<wait 100>
<KeyUp LAlt>